The Pope today described the worldwide Muslim anger that has engulfed his recent remarks about Islam as the result of an "unfortunate misunderstanding".

Benedict XVI said in his weekly address to thousands of pilgrims at the Vatican in Rome that his use of a medieval quotation criticising the use of violence to spread the Muslim faith did not reflect his own opinions.

The controversy which followed his speech at a university in Germany last week has led to violent protests in Muslim countries, Islamic militant death threats against Christians and against the Pope himself, and attacks on churches in the Palestinian territories. Today the Pope said that he hoped the turmoil could eventually serve to encourage "positive and even self-critical dialogue" between religions.

The 79-year-old head of the Roman Catholic Church has already issued an apology, saying on Sunday that he was "deeply sorry" for the reaction to his speech last week at Regensburg University, in which he quoted a medieval Byzantine emperor criticising some teachings of the Prophet Muhammad as "evil and inhuman".

"But for the careful reader of my text it is clear that I in no way wanted to make mine the negative words pronounced by the medieval emperor and their polemical content does not reflect my personal conviction," the Pope said.

"My intention was very different. I wanted to explain that religion and violence do not go together but religion and reason do.

"I trust that after the initial reaction, my words at the University of Regensburg can constitute an impulse and encouragement toward positive, even self-critical dialogue both among religions and between modern reason and Christian faith."

Pope Benedict today also expressed respect for followers of all religions, "particularly Muslims". He said he hoped that on various occasions during his six-day visit, he had made clear his "profound respect for all religions, particularly Muslims, with whom we worship one God and collaborate in defending rights, peace and freedom".

His words came after it emerged that the man who shot and wounded the previous Pope had written to Pope Benedict XVI to urge him not to visit Turkey as planned in November. Mehmet Ali Agca, the Turkish gunman who tried to murder John Paul II in 1981 and is now in prison in Turkey, said: "I write as one who knows about these matters very well…Your life is in danger. Don’t come to Turkey - absolutely not!"

The speech has led to several days of protests in Muslim countries against the Pope, who has since been issued death-threats from a terrorist group linked to al Qaeda. In Somalia, a nun was shot dead. Churches in Palestinian areas have been attacked and security at churches and mosques in the UK and around the world has been increased.

Today The Times revealed that the former Archbishop of Canterbury, Lord Carey of Clifton, had defended the Pope’s speech and issued his own challenge to the Muslim world, which he said had developed a "deep-seated Westophobia" in recent times.

In a lecture titled The Cross and the Crescent: The Clash of Faiths in an Age of Secularism, at Newbold College, Berkshire, Lord Carey said that Muslims had to address "with great urgency" their religion’s association with violence.

"We are living in dangerous and potentially cataclysmic times," he said. "There will be no significant material and economic progress [in Muslim communities] until the Muslim mind is allowed to challenge the status quo of Muslim conventions and even their most cherished shibboleths."

He described the relationship between Islamic countries and the West as "the most dangerous, most important and potentially cataclysmic issue of our day" and said that the Danish cartoons crisis last March showed "two world views colliding in public space with no common point of reference".

Lord Carey went on to defend the Pope’s fundamental thesis, saying: "The actual essay is an extraordinarily effective and lucid thesis exploring the weakness of secularism and the way that faith and reason go hand in hand."

Meanwhile, in a sign that anger about the Pope’s comments had yet to subside, President Pervez Musharraf of Pakistan called for a ban on the "defamation of Islam" in a speech to the United Nations General Assembly in New York.

"We also need to bridge, through dialogue and understanding, the growing divide between the Islamic and Western worlds," General Musharraf told the 192-member assembly.

"It is imperative to end racial and religious discrimination against Muslims and to prohibit the defamation of Islam."

In an apparent reference to the Pope, he said: "It is most disappointing to see personalities of high standing oblivious of Muslim sensitivities at these critical moments."

Other Muslim leaders appeared to be satisfied by the Pope’s apologies for offence caused. Morocco today sent back its ambassador to the Vatican having previously recalled the envoy in protest at the speech, while Mahmoud Ahmadinejad, Iran’s hardline President, told NBC television in New York that "there is no problem" now that the Pope had apologised.

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